An investigation was conducted to ascertain the collapse resistance capacity of the seismic isolation system of prefabricated frame structures (ISPFS). To this end, a representative ISPFS model was designed using PKPM software. A corresponding finite element model was established using ETABS software, and incremental dynamic analysis was conducted. The structural vulnerability characteristics were studied by obtaining fragility curves under four performance levels with inter-story drift as the damage index. The collapse resistance capacity was evaluated using the collapse margin ratio (CMR). The results demonstrate that the ISPFS exhibits three primary failure modes: superstructure failure, rubber bearing failure, and isolation pier (column) failure, with the latter being the dominant collapse mode. The study's findings underscore the critical importance of effectively managing rubber bearing damage in enhancing the system's overall collapse resistance. In the context of rare seismic events, the structure demonstrates a CMR of 3.7, which meets the recommended requirement of 2.7 for structural collapse safety. Additionally, it exhibits exceptional resilience to seismic events, maintaining its structural integrity during rare seismic events.maintains excellent collapse resistance capacity under extremely rare earthquakes.